net.maizegenetics.analysis.distance

Class KinshipPlugin

AbstractPlugin

net.maizegenetics.analysis.distance.KinshipPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class KinshipPlugin
extends AbstractPlugin

Constructor Detail

KinshipPlugin

public KinshipPlugin(java.awt.Frame parentFrame,
                     boolean isInteractive)

Method Detail

preProcessParameters

protected void preProcessParameters(DataSet input)

setParameters

public void setParameters(java.lang.String[] args)

processData

public DataSet processData(DataSet input)

pluginUserManualURL

public java.lang.String pluginUserManualURL()

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

runPlugin

public DistanceMatrix runPlugin(DataSet input)

Convenience method to run plugin with one return object.

runPlugin

public DistanceMatrix runPlugin(GenotypeTable input)

Convenience method to run plugin with one return object.

kinshipMethod

public net.maizegenetics.analysis.distance.KinshipPlugin.KINSHIP_METHOD kinshipMethod()

The scaled_IBS method produces a kinship matrix that is scaled to give a reasonable estimate of additive genetic variance. The pairwise_IBS method, which is the method used by TASSEL ver.4, may result in an inflated estimate of genetic variance. Either will do a good job of controlling population structure in MLM. The pedigree method is used to calculate a kinship matrix from a pedigree information.

Returns:

org.jetbrains.dokka.NodeRenderContent@1f8d5991: Kinship method

kinshipMethod

public KinshipPlugin kinshipMethod(net.maizegenetics.analysis.distance.KinshipPlugin.KINSHIP_METHOD value)

Set Kinship method. The scaled_IBS method produces a kinship matrix that is scaled to give a reasonable estimate of additive genetic variance. The pairwise_IBS method, which is the method used by TASSEL ver.4, may result in an inflated estimate of genetic variance. Either will do a good job of controlling population structure in MLM. The pedigree method is used to calculate a kinship matrix from a pedigree information.

Parameters:

value - Kinship method

Returns:

org.jetbrains.dokka.NodeRenderContent@23592c1b: this plugin

maxAlleles

public java.lang.Integer maxAlleles()

Max Alleles

Returns:

org.jetbrains.dokka.NodeRenderContent@60c7f288: Max Alleles

maxAlleles

public KinshipPlugin maxAlleles(java.lang.Integer value)

Set Max Alleles. Max Alleles

Parameters:

value - Max Alleles

Returns:

org.jetbrains.dokka.NodeRenderContent@27b3b6a7: this plugin

algorithmVariation

public net.maizegenetics.analysis.distance.KinshipPlugin.ALGORITHM_VARIATION algorithmVariation()

Algorithm Variation

Returns:

org.jetbrains.dokka.NodeRenderContent@52073211: Algorithm Variation

algorithmVariation

public KinshipPlugin algorithmVariation(net.maizegenetics.analysis.distance.KinshipPlugin.ALGORITHM_VARIATION value)

Set Algorithm Variation. Algorithm Variation

Parameters:

value - Algorithm Variation

Returns:

org.jetbrains.dokka.NodeRenderContent@38d4f5be: this plugin